Kesel worked with comic book illustrator Brandon McKinney on issues #6 and #13 of the comic series Aliens: Space Marines published by Dark Horse Comics, which accompanied alien figures in the first line of Alien figures released by Kenner in 1992.

In 2000, Kesel and his former Superboy collaborator Tom Grummett created Section Zero as part of the Gorilla Comics imprint at Image Comics. Gorilla Comics was intended to be a creator owned company financed by a comics related website, eHero.com.[13] The website proved to be a financial failure, leaving the creators to personally finance their own books. Along with the other Gorilla Comics creators, Kesel and Grummett attempted to continue the series they started, but these efforts proved to be unsuccessful.[14] In January 2012, Kesel announced that he and Grummett would be relaunching Section Zero as a webcomic on the Mad Genius Comics website.[15][16] The previously published stories were posted on the site and new material was added as it was completed.[17]

^Manning, Matthew K.; Dolan, Hannah, ed. (2010). "1980s". DC Comics Year By Year A Visual Chronicle. London, United Kingdom: Dorling Kindersley. p. 234. ISBN978-0-7566-6742-9. Written by Barbara and Karl Kesel and drawn by future superstar Rob Liefeld, this five-issue miniseries reestablished the famous pair for a new generation.

^Manning "1990s" in Dolan, p. 259: "The issue also featured four teaser comics that introduced a group of contenders all vying for the Superman name...A cloned Superboy escaped captivity in a yarn by writer Karl Kesel and artist Tom Grummett."

^Manning "1990s" in Dolan, p. 265: "Superboy set up camp in picturesque Hawaii in his new ongoing title written by Karl Kesel and with art by Tom Grummett."

^Manning "1990s" in Dolan, p. 274: "In this four-issue miniseries by writer Karl Kesel and artist Stuart Immonnen, the heroes of the present united with the Legion of Super-Heroes and the New Gods in an attempt to stop a 'sun-eater'."